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Conference Papers Year : 2019

Developing infrastructures for FAIR data in plant biology

Cyril Pommier
Guillaume Cornut
  • Function : Author
Michael Alaux
Thomas Letellier
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  • PersonId : 1203739
Célia Michotey
Nacer Mohellibi
Sophie Durand
Erik Kimmel
  • Function : Author
  • PersonId : 1203744
Hadi Quesneville

Abstract

INRA is involved in several EU infrastructures (e.g. ELIXIR, EMPHASIS) or global initiatives (e.g. Wheat Initiative, Research Data Alliance) contributing to the development of : (i) community recommendations for data standardization (e.g. Dzale-Yeumo et al 2017, https://doi.org/10.12688/f1000research.12234.2), (ii) data standards for phenotyping data (www.miappe.org), (iii) crop specific ontologies in the frame of the CropOntology (http://www.cropontology.org/) and (iv) standard web services (www.brapi.org). These global resources are used to capture the data produced in large scientific projects with a standard and structured vocabulary and to store them into INRA’s central repository for plant genomic, phenomic and genetic data, GnpIS (https://urgi.versailles.inra.fr/gnpis/) under the FAIR principles (https://www.force11.org/group/fairgroup/fairprinciples). In parallel, we have developed tools to support federation of databases. The first one is a light data discovery tool based on text indexing technologies, which allows to find data across several distinct databases based on a common high level generic data model (Spannagl et al 2016). The current federates 15 databases from 6 countries (https://urgi.versailles.inra.fr/wheatis/). Another tool allowing data search on phenotyping data and based on BrAPI web services is also about to be released in the frame of the H2020 ELIXIR-Excelerate project, n°676559. The long term resilience and success of such federations will highly depend on the capacity to animate and structure the community working on data for plant biology.
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hal-03316569 , version 1 (06-08-2021)

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Cyril Pommier, Guillaume Cornut, Michael Alaux, Windpouire Esther Dzale Yeumo, Raphaël Flores, et al.. Developing infrastructures for FAIR data in plant biology. Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany. ⟨hal-03316569⟩
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